tbuckley/cabot-search huggingface dataset:
Abstract 3719: Loss of Kmt2c, of the COMPASS-like complex, cooperates with oncogenic signaling in cancer
Authors: Gabriel Prado, Richard L. Bennett, Jonathan D. Licht
Journal: Cancer Research (2022)

Abstract In mammals, the histone methyltransferase KMT2C is one of the major regulators of gene expression and is one of the most commonly lost epigenetic regulators across all cancers. Studies in mice demonstrated that Kmt2c is a haploinsufficient tumor suppressor in AML and inoculation of mammary fat pads with breast cancer cells that lack KMT2C had significantly larger tumor growth and reduced survival compared to mice injected with isogenic wild-type cells. Analysis of cBioportal’s curated set of non-redundant cancer patient studies indicates that loss of function KMT2C mutations significantly co-occur with RAS gain of function mutations. Our lab previously discovered that cells expressing oncogenic RAS displayed altered activation of enhancer gene regulator elements. We will test how loss of KMT2C cooperates with oncogenic Ras by: 1) characterizing the impact of KMT2C loss, with or without expression of oncogenic RAS, on biological properties of cells and global chromatin architecture and 2) characterizing how KMT2C loss may cooperate with oncogenic RAS to alter hematopoiesis and the global enhancer landscape in animal models. MEFs expressing heterozygous loss of Kmt2c have a proliferative advantage relative to WT littermate controls. Interestingly, WT MEFs demonstrate enhanced migration in a wound assay, but heterozygotes demonstrate an advantage in a transwell membrane assay. Heterozygotes further display greater EdU incorporation, indicating a greater propensity for entering S-phase and undergoing cell-division. RNA-seq experiments have indicated an upregulation of MAPK &amp; Ras signaling pathway genes in heterozygotes, whilst simultaneously downregulating gene pathways critical for proper extra-cellular matrix organization. Therefore, loss of Kmt2c disrupts biological cell phenotypes, in a manner relatable to the hallmarks of cancer, demonstrating how Kmt2c loss may promote malignancy. Further studies must now be performed to elucidate the molecular mechanisms altered by loss of KMT2C and how they cause changes in cellular phenotypes. Citation Format: Gabriel Prado, Richard L. Bennett, Jonathan D. Licht. Loss of Kmt2c, of the COMPASS-like complex, cooperates with oncogenic signaling in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3719.
Abstract 1029: The anti-androgen seviteronel sensitizes triple-negative breast cancer to chemotherapy
Authors: Beatriz P. San Juan, Soroor Hediyah-Zadeh, Laura Rangel, Vanina Rodriguez, Heloisa H. Milioli, Felix Kohane, Carley A. Purcell, Therese E. Hickey, Leonard D. Goldstein, John G. Lock, Melissa J. Davis, Christine L. Chaffer
Journal: Cancer Research (2022)

Abstract Therapeutic strategies that improve survival outcomes for advanced-stage breast cancers have proven a major clinical challenge. Here, we define an androgen receptor (AR) signalling network that governs the maintenance and de novo formation of cancer stem cells in triple-negative breast cancer. In response to chemotherapy, AR activation switches cells into a cancer stem cell state, while AR antagonism suppresses cancer stem cell formation and function. In vivo, we validate that the AR antagonist, seviteronel, significantly improves chemotherapy-mediated inhibition of primary and metastatic tumour growth. Analysing three independent triple-negative breast cancer patient cohorts we identify that cytoplasmic AR expression prognosticates poor survival in treatment-naïve patients and predicts poor response to chemotherapy. Additionally, Phase II clinical trial data demonstrates that seviteronel treatment followed by chemotherapy improved survival outcomes in triple-negative breast cancer patients expressing high cytoplasmic AR levels. Seviteronel combined with chemotherapy represents a promising therapeutic strategy for triple-negative breast cancer patients. Citation Format: Beatriz P. San Juan, Soroor Hediyah-Zadeh, Laura Rangel, Vanina Rodriguez, Heloisa H. Milioli, Felix Kohane, Carley A. Purcell, Therese E. Hickey, Leonard D. Goldstein, John G. Lock, Melissa J. Davis, Christine L. Chaffer. The anti-androgen seviteronel sensitizes triple-negative breast cancer to chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1029.
Abstract 3965: Histone H3 K27M mediated regulation of cancer cell stemness and differentiation in diffuse intrinsic pontine glioma (DIPG)
Authors: Monika Sharma, Brian Magnuson, Jeanette Cruz, McKenzie Kauss, Alexander Buschhaus, Mats Ljungman, Stefanie Galban
Journal: Cancer Research (2022)

Abstract Diffuse Intrinsic Pontine Glioma (DIPG) is a rare pediatric brain tumor with a median survival of 10-15 months. Histone H3 is mutated in 80% of DIPGs, dictating tumor location, onset, and outcome of this devastating disease. Therapeutic resistance remains a major obstacle to preventing tumor recurrence and is in part driven by cancer stem cells (CSCs), which exhibit self-renewal properties and tumorigenic potential. In previous studies, we have identified these proliferative and tumorigenic features in aldehyde dehydrogenase positive (ALDH+) CSCs in H3K27M mutant DIPG. Among the 19 ALDH isoforms known in humans, aldehyde dehydrogenase family 1 member A3 (ALDH1A3) is most highly expressed in malignant cells when compared to immune cells or oligodendrocytes in H3K27M DIPG biopsies, indicating an important mechanistic role in regulating stemness in DIPG. We hypothesize that ALDH-mediated cancer stemness and resistance may in part be driven by H3K27M. Indeed, ALDH1A3 expression was dramatically reduced in CRISPR-edited DIPG cells where the H3K27M mutation had been removed (H3K27M-KO). Furthermore, these cells lost their neurosphere forming potential, began to express glial fibrillary acidic protein (GFAP) and attached to the plastic, changes indicative of differentiation. Transcriptomic and GSEA pathway analyses suggested Wnt-dependent regulation of ALDH1A3, with Wnt 7b and Wnt 11 demonstrating the largest difference in the isogenic DIPGs. In addition, DNA repair, along with PI3K/AKT and Wnt signaling, were found to be upregulated upon radiation of DIPG cells, indicating future therapeutic opportunities to prevent radio resistance. We have co-targeted these cell-intrinsic vulnerabilities to eradicate CSCs in DIPG and prevent tumor recurrence, using a combination of radiotherapy, the PI3K/mTOR inhibitor GDC-0084 and the ALDH inhibitor Disulfiram. This combination has produced an exquisite synergy in cells, which we will test in clinically-relevant DIPG models. Taken together, through these studies we have gained mechanistic insight into H3K27M mediated regulation of cancer cell stemness and differentiation in DIPG, which appears to be mediated by Wnt-dependent signaling of ALDH1A3 and provides rationale for exploring new therapeutic targets. Citation Format: Monika Sharma, Brian Magnuson, Jeanette Cruz, McKenzie Kauss, Alexander Buschhaus, Mats Ljungman, Stefanie Galban. Histone H3 K27M mediated regulation of cancer cell stemness and differentiation in diffuse intrinsic pontine glioma (DIPG) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3965.
Abstract 2442: Seminal fluid enhances cervical squamous carcinoma cell proliferation, epithelial mesenchymal transition (EMT), migration &amp; invasion
Authors: Nonkululeko Mkwanazi, Virna D. Leaner, Arieh A. Katz
Journal: Cancer Research (2022)

Abstract Cervical cancer is the leading cause of cancer related deaths &amp; the second most common cancer amongst South African women. Though there are various risk factors, the most common risk factor for cervical cancer development is sexual transmission &amp; persistent infection with high-risk Human Papillomavirus (HPV). Although most HPV infections are cleared naturally in women, persistent infection with high-risk HPV types promotes neoplastic transformation &amp; tumorigenesis. Furthermore, exposure of neoplastic cervical epithelial cells to inflammatory mediators may drive the progression of cervical cancer. Seminal fluid (SF), a biological fluid rich in inflammatory mediators &amp; growth factors, has been implicated in cervical cancer progression. SF has been shown to induce the expression of proinflammatory mediators which promotes cell proliferation in culture &amp; growth of explants in mice injected with HeLa cervical adenocarcinoma cells. Since majority of cervical cancer cases are squamous cell carcinoma, in this study, we examined the effect of SF on cell proliferation, EMT, cell migration &amp; invasion employing SiHa and Me180 squamous cell carcinoma cell lines. Our results showed that SF significantly enhanced cell proliferation in both cell lines. Using Confocal microscopy and phalloidin staining we further showed that SF caused morphological changes and stress fibre formation. RT-qPCR showed that SF up regulated EMT transcription factors Snail, ZEB1 &amp; TWIST mRNA expression. EMT induction was further confirmed by the increase of N-cadherin &amp; a subsequent decrease in E-cadherin protein expression. Additionally, we showed that the induction of EMT transcription factors by SF occurs via the EGF/ERK/COX pathway. To investigate the effect of SF on migration and invasion, transwell migration assays were used. Results showed that SF significantly enhanced cell migration &amp; invasion of the SiHa and Me180 cells. Our results show that SF plays a role in enhancing the migratory &amp; invasive potential of squamous cell carcinoma cells &amp; that this associates with increased expression of EMT transcription factors. These findings together implicate SF as a possible factor that may promote cervical cancer progression. Citation Format: Nonkululeko Mkwanazi, Virna D. Leaner, Arieh A. Katz. Seminal fluid enhances cervical squamous carcinoma cell proliferation, epithelial mesenchymal transition (EMT), migration &amp; invasion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2442.
Abstract 3913: Quantitative phosphoproteomic analysis of AXL signaling network in breast cancer
Authors: Li Wang, Nicole Pearson, Yuning Xiong, Santosh Renuse, Ran Cheng, Jodi M. Carter, Akhilesh Pandey, Xinyan Wu
Journal: Cancer Research (2022)

Abstract Background: As a key receptor tyrosine kinase (RTK) regulating tumorigenesis, AXL is overexpressed in multiple different types of cancers. AXL can be activated by homodimerization after binding with its ligand, growth arrest specific 6 protein (Gas6) or by heterodimerization with other RTKs. AXL overexpression and/or activation have been reported to promote cancer cell proliferation, migration/invasion and to induce resistance to targeted therapy. However, the AXL downstream signaling network has not yet been fully elucidated. Methods: We employed a CRISPR-CAS9-based knockout technology to create AXL inducible knockout cells in a human triple negative breast cancer (TNBC) cell line, HCC1395. In order to explore the downstream signaling events driven by AXL, we induced AXL knockout for 72 hours and used a 6-plex TMT-labeling-based quantitative proteomic approach to characterize the protein phosphorylation alterations induced by AXL knockout. IMAC and anti-phosphotyrosine antibody (pY1000)-based phosphopeptide enrichment methods were used to comprehensively quantify the phosphoproteome changes induced by AXL knockout. Results: In this study, we identified 38,525 phospho serine/threonine sites and 1,427 phosphotyrosine sites. In response to AXL knockout, 1,581 phospho serine/threonine sites and 40 phosphotyrosine sites showed significant differences between AXL-KO and AXL-WT groups with &amp;gt;1.5-fold change and p&amp;lt;0.05 as the cutoff. Among them, 982 phosphoserine/threonine sites and 30 phosphotyrosine sites were decreased, while 599 phospho serine/threonine sites and 10 phosphotyrosine sites were increased in AXL-KO cells. Signaling pathway enrichment analysis revealed that suppressing AXL expression could inhibit multiple important cancer related signaling pathways, including cell cycle, focal adhesion, MAPK signaling pathway, p53 signaling pathway and mTOR signaling pathway. Conclusion: Quantitative analysis of the phosphoproteome driven by AXL demonstrated that AXL plays a pivotal role in regulating canonical oncogenic signaling but also signaling pathways involved in RNA processing and DNA repair. Our data also suggest that targeting AXL could suppress these oncogenic signaling pathways and have therapeutic potential to improve clinical outcomes for patients with AXL overexpression. Citation Format: Li Wang, Nicole Pearson, Yuning Xiong, Santosh Renuse, Ran Cheng, Jodi M. Carter, Akhilesh Pandey, Xinyan Wu. Quantitative phosphoproteomic analysis of AXL signaling network in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3913.
Finding the right help in the tumor microenvironment
Authors: Jessica N. Filderman, Walter J. Storkus
Journal: Journal of Clinical Investigation (2022)

Tumor-infiltrating lymphocytes (TILs) contain substantial numbers of CD4+ T cells mediating pro- and antitumor functions. While CD4+ Tregs are well characterized and known to promote tumor immune evasion, the fingerprint of CD4+ Th cells that recognizes tumor antigens and serves to restrict disease progression has remained poorly discriminated. In this issue of the JCI, Duhen et al. analyzed tumors from patients with head and neck squamous cell carcinoma or colon carcinoma and identified a unique programmed cell death 1–positive, ICOS1-positive (PD-1+ICOS1+) subpopulation of CD4+ TILs highly enriched for the ability to recognize tumor-associated antigens. These cells localized proximally to MHC II+ antigen-presenting cells and CD8+ T cells within tumors, where they appeared to proliferate and function almost exclusively as Th cells. These potentially therapeutic Th cells can be monitored for patient prognosis and are expected to have substantial utility in developing personalized adoptive cell– and vaccine-based immunotherapeutic approaches for improving patient outcomes.
Circulating Tumor Cells for the Staging of Patients With Newly Diagnosed Transplant-Eligible Multiple Myeloma
Authors: Juan-Jose Garcés, Maria-Teresa Cedena, Noemi Puig, Leire Burgos, Jose J. Perez, Lourdes Cordon, Juan Flores-Montero, Luzalba Sanoja-Flores, Maria-Jose Calasanz, Albert Ortiol, María-Jesús Blanchard, Rafael Rios, Jesus Martin, Rafael Martínez-Martinez, Joan Bargay, Anna Sureda, Javier de la Rubia, Miguel-Teodoro Hernandez, Paula Rodriguez-Otero, Javier de la Cruz, Alberto Orfao, Maria-Victoria Mateos, Joaquin Martinez-Lopez, Juan-Jose Lahuerta, Laura Rosiñol, Joan Blade, Jesus F. San-Miguel, Bruno Paiva
Journal: Journal of Clinical Oncology (2022)

PURPOSE Patients with multiple myeloma (MM) may show patchy bone marrow (BM) infiltration and extramedullary disease. Notwithstanding, quantification of plasma cells (PCs) continues to be performed in BM since the clinical translation of circulating tumor cells (CTCs) remains undefined. PATIENTS AND METHODS CTCs were measured in peripheral blood (PB) of 374 patients with newly diagnosed MM enrolled in the GEM2012MENOS65 and GEM2014MAIN trials. Treatment included bortezomib, lenalidomide, and dexamethasone induction followed by autologous transplant, consolidation, and maintenance. Next-generation flow cytometry was used to evaluate CTCs in PB at diagnosis and measurable residual disease (MRD) in BM throughout treatment. RESULTS CTCs were detected in 92% (344 of 374) of patients with newly diagnosed MM. The correlation between the percentages of CTCs and BM PCs was modest. Increasing logarithmic percentages of CTCs were associated with inferior progression-free survival (PFS). A cutoff of 0.01% CTCs showed an independent prognostic value (hazard ratio: 2.02; 95% CI, 1.3 to 3.1; P = .001) in multivariable PFS analysis including the International Staging System, lactate dehydrogenase levels, and cytogenetics. The combination of the four prognostic factors significantly improved risk stratification. Outcomes according to the percentage of CTCs and depth of response to treatment showed that patients with undetectable CTCs had exceptional PFS regardless of complete remission and MRD status. In all other cases with detectable CTCs, only achieving MRD negativity (and not complete remission) demonstrated a statistically significant increase in PFS. CONCLUSION Evaluation of CTCs in PB outperformed quantification of BM PCs. The detection of ≥ 0.01% CTCs could be a new risk factor in novel staging systems for patients with transplant-eligible MM.
Abstract 6310: Designing genomic test reports using a user-centered approach for clinicians in Pakistan
Authors: Momal Agha, Faisal Khan
Journal: Cancer Research (2022)

Abstract In the developed world, precision medicine and genomics are transforming traditional healthcare approaches. In spite of rapid technological progress being made in genomics, a 'genomic divide' is emerging between developed and developing countries. This is partly because of the limited genomic literacy of healthcare professionals and a scarcity of available genomics workforce that reportedly deters them from proposing genomic testing. We aim to help reduce this 'genomic divide' by proposing a genomic test report design for clinicians in Pakistan, that incorporates user-centered design principles. We tested two commonly used genomic reportswiththat varied in language, content and layout. Report A was a one-page genomic report from the Laboratory for Molecular Medicine, of a patient with suspected hypertrophic cardiomyopathy. Report B was a report from FoundationOneCDx, of a breast carcinoma specimen with confirmed findings mentioned. We employed a qualitative descriptive study design, including a survey for trainees, non-specialists, and specialists. The parameters recorded were: subject comprehension, overall visual impression, level of difficulty of the language, and ease of understanding, along with, actionability and degree of trust. A total of 49 medical professionals across 11 institutes in Pakistan participated in the survey, of which 11 were specialists and 38 were non-specialists. We extracted 19 recommendations from the survey and broadly grouped them into three categories: communication style, report content, and layout. About 25% of the respondents commented that they would prefer a short and concise report, 20.8% wanted the language to be ‘doctor-friendly’ and 8.3% preferred data to be presented in tables. All recommendations were incorporated into our proposed genomic test report template. The template displays the results and what they mean for the patient (in layman's terms for ease of access to non-specialists), what possible action is to be taken by the doctor, and details of further information and support regarding the results. We propose the addition of a box on technical methodology at the end of the report template that may help in assisting with refreshing the genomic knowledge of non-specialists. Our findings have shown that in order to design impactful genomic reports for clinicians in Pakistan, we will have to start with a user-centered design approach. This can be instrumental in helping us improve the adoption of genomic testing in clinics around Pakistan. Citation Format: Momal Agha, Faisal Khan. Designing genomic test reports using a user-centered approach for clinicians in Pakistan [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6310.
Abstract 2947: Surveying the tumor suppressive genetic network underlying chr4p deletion in TNBC
Authors: Joseph Del Corpo, Rohan Dandage, Lea Harrington, Elena Kuzmin
Journal: Cancer Research (2022)

Abstract Triple negative breast cancer (TNBC) is a breast cancer subtype lacking targetable biomarkers, resulting in the worst prognosis compared to other breast cancer subtypes. TNBC is characterized by many large copy number variants that result in the deletion and amplifications of many genes, with TP53 being the only common oncogenic driver. Using TCGA data and in-depth functional genomic analysis of TNBC patient-derived xenografts (PDX), our group showed that chr4p is a recurrently deleted region in basal breast cancer, which TNBC is an enriched subtype. This correlated with poor prognosis and a highly proliferative state. Here, we set out to survey the tumor suppressive genetic network underlying the TNBC-specific chr4pdeletion. Using an arrayed CRISPR-enCas12 screening approach, I will generate a panel of mutant cell lines deleted for all protein-coding genes residing within chr4p. MCF10A series of cell lines will be used for mutant cell line construction, because it is an established normal human breast epithelial model system with a normal karyotype to ensure the diploid state ofchr4p and includes other derivatives (MCF10A(-E7-Bcl2)) that show basal anchorage independent growth in 3D to assess cell transformation. The resulting panel of single gene deletion mutant cell lines will be characterized for their effects on proliferation, apoptosis, cell transformation and senescence. Additionally, the tumor suppressive genetic interaction network of chr4p will be mapped using a multiplexed CRISPR-enCas12 screening methodology. A dual guide-RNA library will be generated for all protein-coding genes to test all pairwise combinations for tumor suppressive genetic interactions. The proliferation due to double gene deletions will be monitored and compared to single gene deletions to identify tumor suppressive interactions. This study will be the first to systematically identify tumor suppressor genetic network underlying chr4p. Ultimately, it will provide an in-depth understanding of the genetic network of large copy number variants in TNBC and insight into new avenues for precision oncology. Citation Format: Joseph Del Corpo, Rohan Dandage, Lea Harrington, Elena Kuzmin. Surveying the tumor suppressive genetic network underlying chr4p deletion in TNBC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2947.